[R] making a barplot with table of experimental conditions underneath (preferably ggplot2)

[John Kane]

Hi Nina, 
I think the following code does what you want (thanks to Jim Lemon for showing me what you wanted in terms of x-axis tick labels)

However I  think that barcharts are generally evil  so I changed your geom_bar to geom_point.  Feel free to change it back if your discipline requires it but I think it shows your data better

Also you were doing some unnecessary extraction of dat from the data.frame so I just included a "data =" statement in qplot and changed the variable names in it to the original df names. This makes for cleaner and more readable code.

df <- data.frame (experiment=c("E1","E2","E3","E4"), mean = c(3,4,5,6),
stdev=c(0.1,0.1,0.05,0.2), method = c("STD","STD", "FP", "FP"), enzyme =c
("T","T/L","T","T/L"), denaturation=c("U","U","0.05%RG", "0.1%RG"))

df$labs  <-  paste(df[,4],"\n ",df[,5], "\n ",df[,6]) # create labels

df.plot <- qplot(experiment,mean,data = df, xlab="", ylab="# peptides identified")+
  geom_point(fill="grey")+
  geom_errorbar(aes(x=experiment, ymin=mean-stdev, ymax=mean+stdev), width=0.25)

p + scale_x_discrete( labels = df$labs)

I hop
John Kane
Kingston ON Canada


> -----Original Message-----
> From: n.hubner at ncmls.ru.nl
> Sent: Wed, 13 Nov 2013 14:24:28 +0000
> To: r-help at r-project.org
> Subject: [R] making a barplot with table of experimental conditions
> underneath (preferably ggplot2)
> 
> Dear all,
>
> my data looks the following:
> 
> df <- data.frame (experiment=c("E1","E2","E3","E4"), mean = c(3,4,5,6),
> stdev=c(0.1,0.1,0.05,0.2), method = c("STD","STD", "FP", "FP"), enzyme =c
> ("T","T/L","T","T/L"), denaturation=c("U","U","0.05%RG", "0.1%RG"))

> I would like to make a bar plot with standard deviation which I solved
> the following way:
> 
> x <- df$experiment
> y <- df$mean
> sd <- df$stdev
> 
> df.plot <- qplot(x,y,xlab="", ylab="# peptides identified")+
>   geom_bar(colour="black", fill="darkgrey")+
>   geom_errorbar(aes(x=x, ymin=y-sd, ymax=y+sd), width=0.25)
> 
> df.plot
> 

> However, as the labels for the x-axis (the bars) I do not want the
> experiment number, as now, but instead a table containing the other
> columns of my data.frame (method, enzyme, denaturation) with the
> description in the front and the certain 'value' below the bars.
> 
> I am looking forward to your suggestions!
>
> With best wishes,
> 
> Nina
> ______________________________________________
> 
> Dr. Nina C. Hubner
> scientist quantitative proteomics
> 
> Dep. of Molecular Biology, Radboud University Nijmegen, The Netherlands
> e-mail: n.hubner at ncmls.ru.nl
> tel: +31-24-3613655
> 
> Visiting address:
> NCMLS, Dept of Molecular Biology (route 274)
> Geert Grooteplein 26/28
> 6525 GA Nijmegen
> The Netherlands
> 
> 
> 
> 
> The Radboud University Medical Centre is listed in the Commercial
> Register of the Chamber of Commerce under file number 41055629.
> 
> 
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